BtaINT0158389 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020311 | USP20
Description
Bos taurus ubiquitin specific peptidase 20 (USP20), mRNA. [Source:RefSeq mRNA;Acc:NM_001105333]
Coordinates
chr11:100274414-100274799:+
Coord C1 exon
chr11:100274414-100274594
Coord A exon
chr11:100274595-100274672
Coord C2 exon
chr11:100274673-100274799
Length
78 bp
Sequences
Splice sites
5' ss Seq
GCAGTGAGT
5' ss Score
7.39
3' ss Seq
GCCTGAGTCTCCCGTCGCAGGTG
3' ss Score
6.63
Exon sequences
Seq C1 exon
ATCCTGTGCATTCACCTGAAGCGCTTTAGGCACGAGGTCATGTACTCTTTCAAGATCAGCAGCCATGTGTCCTTCCCCCTCGAGGGCCTTGACCTGCGCCCCTTCCTCGCCAAGGAGTGCACGTCCCAGATCACCACCTATGACCTCCTCTCGGTCATCTGCCACCACGGCACGGCAGGCA
Seq A exon
GTGAGTCCGCGCCCGCCCCTGCCCCGACCCCGCCCAGTCCCCTGGGGGCTCCATCACCGCCTGAGTCTCCCGTCGCAG
Seq C2 exon
GTGGCCACTACATCGCCTACTGCCAGAACGTGATCAACGGGCAGTGGTATGAGTTCGACGACCAGTACGTCACCGAGGTCCACGAGACGGTGGTGCAGAACGCGGAGGCCTACGTGCTCTTCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020311:ENSBTAT00000027070:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0044324=UCH=FE(11.2=100)
A:
NA
C2:
PF0044324=UCH=PD(7.6=95.3),PF063377=DUSP=PU(25.8=79.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACCTATGACCTCCTCTCGG
R:
TAGAAGAGCACGTAGGCCTCC
Band lengths:
172-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development